# This file created by conda-build 24.7.1
# meta.yaml template originally from:
# /opt/recipe, last modified Sun Nov 10 14:11:31 2024
# ------------------------------------------------

package:
  name: quast
  version: 5.3.0
source:
  patches:
    - genemark-issue_disable-and-exclude-from-package.patch
    - remove-explicit-dependencies-from-setup-py.patch
    - skip-glimmer-in-test.patch
  sha256: ac9dba03ef9d0a51d7a9e2c56826104e78f340f6263a3ad393648442debc74ec
  url:
    - http://downloads.sourceforge.net/project/quast/quast-5.3.0.tar.gz
    - https://github.com/ablab/quast/releases/download/quast_5.3.0/quast-5.3.0.tar.gz
build:
  number: '0'
  run_exports:
    - quast >=5.3.0,<5.4.0a0
  string: py312pl5321hc60241a_0
requirements:
  build:
    - _libgcc_mutex 0.1 conda_forge
    - _openmp_mutex 4.5 2_gnu
    - binutils_impl_linux-64 2.43 h4bf12b8_2
    - binutils_linux-64 2.43 h4852527_2
    - gcc_impl_linux-64 12.4.0 hb2e57f8_1
    - gcc_linux-64 12.4.0 h6b7512a_5
    - gxx_impl_linux-64 12.4.0 h613a52c_1
    - gxx_linux-64 12.4.0 h8489865_5
    - kernel-headers_linux-64 3.10.0 he073ed8_18
    - ld_impl_linux-64 2.43 h712a8e2_2
    - libgcc 14.2.0 h77fa898_1
    - libgcc-devel_linux-64 12.4.0 ha4f9413_101
    - libgomp 14.2.0 h77fa898_1
    - libsanitizer 12.4.0 h46f95d5_1
    - libstdcxx 14.2.0 hc0a3c3a_1
    - libstdcxx-devel_linux-64 12.4.0 ha4f9413_101
    - make 4.4.1 hb9d3cd8_2
    - sysroot_linux-64 2.17 h4a8ded7_18
    - tzdata 2024b hc8b5060_0
  host:
    - _libgcc_mutex 0.1 conda_forge
    - _openmp_mutex 4.5 2_gnu
    - blast 2.16.0 hc155240_2
    - brotli 1.1.0 hb9d3cd8_2
    - brotli-bin 1.1.0 hb9d3cd8_2
    - bzip2 1.0.8 h4bc722e_7
    - c-ares 1.32.3 h4bc722e_0
    - ca-certificates 2024.8.30 hbcca054_0
    - certifi 2024.8.30 pyhd8ed1ab_0
    - circos 0.69.9 hdfd78af_0
    - contourpy 1.3.0 py312h68727a3_2
    - curl 8.8.0 he654da7_1
    - cycler 0.12.1 pyhd8ed1ab_0
    - entrez-direct 22.4 he881be0_0
    - expat 2.6.4 h5888daf_0
    - font-ttf-dejavu-sans-mono 2.37 hab24e00_0
    - font-ttf-inconsolata 3.000 h77eed37_0
    - font-ttf-source-code-pro 2.038 h77eed37_0
    - font-ttf-ubuntu 0.83 h77eed37_3
    - fontconfig 2.14.2 h14ed4e7_0
    - fonts-conda-ecosystem 1 0
    - fonts-conda-forge 1 0
    - fonttools 4.54.1 py312h178313f_1
    - freetype 2.12.1 h267a509_2
    - gettext 0.22.5 he02047a_3
    - gettext-tools 0.22.5 he02047a_3
    - giflib 5.2.2 hd590300_0
    - glimmerhmm 3.0.4 pl5321hdbdd923_8
    - icu 73.2 h59595ed_0
    - joblib 1.4.2 pyhd8ed1ab_0
    - k8 1.2 h6618dc6_3
    - kernel-headers_linux-64 3.10.0 he073ed8_18
    - keyutils 1.6.1 h166bdaf_0
    - kiwisolver 1.4.7 py312h68727a3_0
    - krb5 1.21.3 h659f571_0
    - lcms2 2.16 hb7c19ff_0
    - ld_impl_linux-64 2.43 h712a8e2_2
    - lerc 4.0.0 h27087fc_0
    - libasprintf 0.22.5 he8f35ee_3
    - libasprintf-devel 0.22.5 he8f35ee_3
    - libblas 3.9.0 25_linux64_openblas
    - libbrotlicommon 1.1.0 hb9d3cd8_2
    - libbrotlidec 1.1.0 hb9d3cd8_2
    - libbrotlienc 1.1.0 hb9d3cd8_2
    - libcblas 3.9.0 25_linux64_openblas
    - libcurl 8.8.0 hca28451_1
    - libdeflate 1.20 hd590300_0
    - libedit 3.1.20191231 he28a2e2_2
    - libev 4.33 hd590300_2
    - libexpat 2.6.4 h5888daf_0
    - libffi 3.4.2 h7f98852_5
    - libgcc 14.2.0 h77fa898_1
    - libgcc-ng 14.2.0 h69a702a_1
    - libgd 2.3.3 h119a65a_9
    - libgettextpo 0.22.5 he02047a_3
    - libgettextpo-devel 0.22.5 he02047a_3
    - libgfortran 14.2.0 h69a702a_1
    - libgfortran5 14.2.0 hd5240d6_1
    - libgomp 14.2.0 h77fa898_1
    - libidn2 2.3.7 hd590300_0
    - libjpeg-turbo 3.0.0 hd590300_1
    - liblapack 3.9.0 25_linux64_openblas
    - libnghttp2 1.58.0 h47da74e_1
    - libnsl 2.0.1 hd590300_0
    - libopenblas 0.3.28 pthreads_h94d23a6_1
    - libpng 1.6.43 h2797004_0
    - libsqlite 3.46.0 hde9e2c9_0
    - libssh2 1.11.0 h0841786_0
    - libstdcxx 14.2.0 hc0a3c3a_1
    - libstdcxx-ng 14.2.0 h4852527_1
    - libtiff 4.6.0 h1dd3fc0_3
    - libunistring 0.9.10 h7f98852_0
    - libuuid 2.38.1 h0b41bf4_0
    - libwebp 1.4.0 h2c329e2_0
    - libwebp-base 1.4.0 hd590300_0
    - libxcb 1.15 h0b41bf4_0
    - libxcrypt 4.4.36 hd590300_1
    - libzlib 1.2.13 h4ab18f5_6
    - matplotlib-base 3.9.2 py312hd3ec401_2
    - minimap2 2.28 he4a0461_3
    - munkres 1.1.4 pyh9f0ad1d_0
    - ncbi-vdb 3.1.1 h4ac6f70_2
    - ncurses 6.5 he02047a_1
    - numpy 2.1.3 py312h58c1407_0
    - openjpeg 2.5.2 h488ebb8_0
    - openssl 3.3.2 hb9d3cd8_0
    - packaging 24.1 pyhd8ed1ab_0
    - perl 5.32.1 7_hd590300_perl5
    - perl-archive-tar 2.40 pl5321hdfd78af_0
    - perl-b-cow 0.007 pl5321hd590300_0
    - perl-carp 1.50 pl5321hd8ed1ab_0
    - perl-clone 0.46 pl5321h166bdaf_0
    - perl-common-sense 3.75 pl5321hd8ed1ab_0
    - perl-compress-raw-bzip2 2.201 pl5321hbf60520_0
    - perl-compress-raw-zlib 2.202 pl5321hadc24fc_0
    - perl-config-general 2.65 pl5321hdfd78af_0
    - perl-digest-perl-md5 1.9 pl5321hdfd78af_2
    - perl-encode 3.21 pl5321hb9d3cd8_1
    - perl-exporter 5.74 pl5321hd8ed1ab_0
    - perl-exporter-tiny 1.002002 pl5321hd8ed1ab_0
    - perl-extutils-config 0.008 pl5321ha770c72_0
    - perl-extutils-helpers 0.026 pl5321ha770c72_0
    - perl-extutils-installpaths 0.012 pl5321ha770c72_0
    - perl-extutils-makemaker 7.70 pl5321hd8ed1ab_0
    - perl-extutils-pl2bat 0.005 pl5321ha770c72_0
    - perl-font-ttf 1.06 pl5321hdfd78af_1
    - perl-gd 2.76 pl5321h5b5514e_1
    - perl-inc-latest 0.500 pl5321ha770c72_0
    - perl-io-compress 2.201 pl5321hdbdd923_2
    - perl-io-string 1.08 pl5321hdfd78af_4
    - perl-io-zlib 1.14 pl5321hdfd78af_0
    - perl-json 4.10 pl5321hdfd78af_1
    - perl-json-xs 4.03 pl5321h4ac6f70_3
    - perl-list-moreutils 0.430 pl5321hdfd78af_0
    - perl-list-moreutils-xs 0.430 pl5321h031d066_3
    - perl-math-bezier 0.01 pl5321hdfd78af_2
    - perl-math-round 0.07 pl5321ha770c72_0
    - perl-math-vecstat 0.08 pl5321hdfd78af_2
    - perl-module-build 0.4232 pl5321ha770c72_0
    - perl-module-build-tiny 0.039 pl5321h166bdaf_0
    - perl-module-implementation 0.09 pl5321ha770c72_0
    - perl-module-runtime 0.016 pl5321ha770c72_0
    - perl-number-format 1.76 pl5321hd8ed1ab_0
    - perl-params-validate 1.31 pl5321hec16e2b_0
    - perl-parent 0.242 pl5321hd8ed1ab_0
    - perl-pathtools 3.75 pl5321h166bdaf_0
    - perl-readonly 2.05 pl5321ha770c72_0
    - perl-regexp-common 2017060201 pl5321hd8ed1ab_0
    - perl-scalar-list-utils 1.68 pl5321hb9d3cd8_0
    - perl-set-intspan 1.19 pl5321hdfd78af_2
    - perl-statistics-basic 1.6611 pl5321hdfd78af_3
    - perl-storable 3.15 pl5321hb9d3cd8_0
    - perl-svg 2.87 pl5321hd8ed1ab_0
    - perl-test-fatal 0.016 pl5321ha770c72_0
    - perl-text-format 0.62 pl5321hdfd78af_0
    - perl-time-hires 1.9764 pl5321h031d066_5
    - perl-try-tiny 0.31 pl5321ha770c72_0
    - perl-types-serialiser 1.01 pl5321hdfd78af_0
    - perl-xml-parser 2.44_01 pl5321hc3e0081_1003
    - pillow 10.3.0 py312hdcec9eb_0
    - pip 24.3.1 pyh8b19718_0
    - pthread-stubs 0.4 hb9d3cd8_1002
    - pyparsing 3.2.0 pyhd8ed1ab_1
    - python 3.12.3 hab00c5b_0_cpython
    - python-dateutil 2.9.0 pyhd8ed1ab_0
    - python_abi 3.12 5_cp312
    - qhull 2020.2 h434a139_5
    - readline 8.2 h8228510_1
    - rpsbproc 0.5.0 h6a68c12_1
    - setuptools 75.3.0 pyhd8ed1ab_0
    - simplejson 3.19.3 py312h66e93f0_1
    - six 1.16.0 pyh6c4a22f_0
    - sysroot_linux-64 2.17 h4a8ded7_18
    - tk 8.6.13 noxft_h4845f30_101
    - tzdata 2024b hc8b5060_0
    - unicodedata2 15.1.0 py312h66e93f0_1
    - wget 1.21.4 hda4d442_0
    - wheel 0.45.0 pyhd8ed1ab_0
    - xorg-libxau 1.0.11 hb9d3cd8_1
    - xorg-libxdmcp 1.1.5 hb9d3cd8_0
    - xz 5.2.6 h166bdaf_0
    - zlib 1.2.13 h4ab18f5_6
    - zstd 1.5.6 ha6fb4c9_0
  run:
    - bedtools
    - blast >=2.16.0,<2.17.0a0
    - bwa
    - circos
    - glimmerHMM
    - joblib
    - libgcc >=12
    - libstdcxx >=12
    - libzlib >=1.2.13,<2.0a0
    - matplotlib-base
    - minimap2 >=2.10
    - minimap2 >=2.28,<3.0a0
    - openjdk >=8
    - perl >=5.32.1,<5.33.0a0 *_perl5
    - python >=3.12,<3.13.0a0
    - python_abi 3.12.* *_cp312
    - simplejson
test:
  commands:
    - quast --version
    - metaquast --version
  source_files:
    - test_data
about:
  home: http://quast.sourceforge.net/
  license: Custom
  license_file: LICENSE.txt
  summary: Quality Assessment Tool for Genome Assemblies
extra:
  container:
    extended-base: true
  copy_test_source_files: true
  final: true
  identifiers:
    - biotools:quast
    - doi:10.1093/bioinformatics/btt086
  notes: '- GeneMark gene prediction software is disabled due to licensing issues

    '
